You're Not Sleeping Because Nobody Fixed the Actual Problem

By Dr. Matt Altman, MD | Rooted Health Clinic, Central Texas

You already know the sleep hygiene list. Dark room. Cool temperature. No screens. No caffeine after 2 PM. White noise machine.

And you're still staring at the ceiling at 2 AM.

Here's the thing — roughly a third of the patients I see have sleep as a primary complaint. Almost every single one has already tried that list. Many have been handed a prescription for Ambien or trazodone. And they're still not sleeping.

That's because sleep hygiene isn't wrong. It's just incomplete. Telling someone with a wrecked cortisol rhythm to "keep their room cool" is like telling someone with a broken leg to try better shoes. You're treating the symptom while the physiology screams underneath.

Where Sleep Fits in the Bigger Picture

Before I get into the specifics, I want to zoom out — because sleep doesn't exist in a vacuum.

In my clinic, I think about health through what I call the Pillars of Health: sleep, diet, exercise, environmental health, community, mental health, and hydration. These pillars are the foundation. When they're solid, your body works the way it's supposed to. When they're cracked, everything downstream — hormones, immune function, mental clarity — starts falling apart.

Sleep is arguably the most foundational of all of them. It's when your brain clears metabolic waste through the glymphatic system. Growth hormone peaks during deep sleep. Your immune system recalibrates. Memories consolidate. Your circadian rhythm drives hormonal health across the board. Without quality sleep, the other pillars can't hold weight.

But here's where it gets real. Some patients walk into my office so depleted — exhausted, in pain, barely functioning — that telling them to "fix their sleep hygiene" is almost insulting. They can barely get through the day. You can't hand someone who hasn't slept properly in two years a list of lifestyle changes and expect them to execute.

So sometimes you have to jump above the pillars. You intervene medically first — address the cortisol, stabilize the blood sugar, correct the deficiency — to get that patient functional enough to then build the foundation properly. It's not a straight line. You meet people where they are.

The Three Tiers: How I Actually Think About Sleep Problems

The way I think about any health issue — sleep included — is through a three-tier framework.

Tier 1 is the foundation: gut health, metabolic health (which includes thyroid function), and HPA axis regulation. This is where I start with almost every sleep patient, because this is where most of the answers live.

Tier 2 goes deeper: environmental exposures, toxins, food sensitivities, hormonal imbalances. Some of these bleed into Tier 1 — hormones especially can straddle both — but generally, these are the factors you investigate once the foundation has been addressed or when the history points you there early.

Tier 3 is the complex stuff: genetics, structural issues, things that require specialized testing and intervention.

For sleep specifically, about 70-80% of what I see gets resolved at Tier 1. So let's talk about what's actually going wrong there.

Cortisol: The Sleep Wrecker Nobody Checks

Let me introduce the HPA axis — your hypothalamic-pituitary-adrenal axis. Think of it as your body's central stress response system. It controls cortisol, your primary stress hormone, and cortisol follows a rhythm throughout the day. It should peak in the morning — that's what wakes you up and makes you feel alert — and gradually decline until evening, when it hits its lowest point and melatonin rises to let sleep happen naturally.

So what happens when that rhythm is broken? Three patterns I see constantly:

The "wired at night" pattern. Cortisol is pumping at 10 PM when it should be at rock bottom. Racing thoughts. Can't shut off. Classic tired-and-wired.

The flat curve. Exhausted all day AND can't sleep at night. Cortisol never peaks properly in the morning, never drops properly at night. The entire rhythm has just... flattened. Some practitioners call this "adrenal fatigue" — conventional medicine doesn't love that term, but the underlying HPA axis dysregulation is well-documented in the literature.

The early morning spike. Falls asleep fine, then bolt awake at 2-4 AM and can't get back to sleep. Cortisol is surging hours too early.

None of these respond to a sleep hygiene checklist. You have to address the HPA axis directly. And that naturally leads to the next piece, because one of the biggest drivers of that cortisol disruption is something embarrassingly simple.

Blood Sugar Is Waking You Up at 2 AM

This one is huge.

When you eat a high-carb dinner or a sugary snack before bed, your blood sugar spikes and then crashes in the middle of the night. When blood sugar drops too low — what we call a nocturnal hypoglycemic episode — your body releases cortisol and adrenaline to bring it back up.

That's an adrenaline surge. At 2 AM.

You wake up with your heart pounding. Maybe sweating. Feeling anxious. You think it's stress. It's actually your blood sugar.

I can't tell you how many patients I've helped simply by changing what they eat at dinner and adding a small protein-and-fat snack before bed. No prescription needed. Just macronutrient timing. A tablespoon of almond butter. A few bites of leftover meat. That's it.

Research backs this up — a 2020 study in the *American Journal of Clinical Nutrition* found that higher glycemic index diets were significantly associated with insomnia, particularly in postmenopausal women. The mechanism is exactly what I just described: blood sugar instability triggering counter-regulatory hormonal responses during sleep.

And this connects directly back to the metabolic health piece in Tier 1. If someone has insulin resistance — which is incredibly common and often undiagnosed — their blood sugar regulation is already compromised. Fixing sleep sometimes starts with fixing metabolism.

Inflammation: The Quiet Sleep Thief

Here's where gut health enters the picture — another Tier 1 foundation.

When you have chronic systemic inflammation — from gut issues, autoimmune conditions, metabolic syndrome, chronic stress — it directly disrupts your sleep architecture. Pro-inflammatory cytokines, the signaling molecules your immune system produces, reduce deep restorative sleep, fragment your sleep cycles, and increase daytime sleepiness.

Think about the last time you were really sick. Exhausted but couldn't sleep well. Restless. Fragmented. That's inflammation disrupting sleep in real-time. Now imagine a low-grade version of that running in the background every single night. Not enough to make you feel "sick," but enough to keep you from ever getting truly restorative sleep.

A major study in *Nature Reviews Immunology* confirmed that even mild elevations in inflammatory markers like CRP — that's C-reactive protein, a basic blood test for inflammation — are associated with poorer sleep quality and more nighttime awakenings.

So when I'm working up a sleep patient, I'm not just asking about their bedtime routine. I'm looking at their gut. I'm checking inflammatory markers. I'm asking about their diet. Because the inflammation driving their sleep disruption might be coming from a place they'd never connect to sleep.

The Labs Your Doctor Didn't Run

When someone comes to me with sleep problems, I'm ordering labs that most doctors skip entirely:

Full thyroid panel. Not just TSH. I want free T3, free T4, reverse T3, and thyroid antibodies. Both hypothyroid and hyperthyroid states wreck sleep, and subclinical thyroid dysfunction — where TSH looks "normal" but the full picture is off — is incredibly common. Ideal TSH for me is somewhere between 0.3 and 2. Anything above that, especially if the patient is symptomatic, and I'm looking deeper.

Ferritin. This is iron storage. Low ferritin — even when hemoglobin is technically "normal" — is a major driver of restless leg syndrome and sleep disruption. I see ferritin levels of 15-20 ng/mL labeled as "normal" all the time when optimal is more like 50-100. That gap is the difference between sleeping through the night and kicking your partner awake.

RBC magnesium. Not serum magnesium — that's almost useless because it's so tightly regulated. RBC magnesium gives you the real picture. Magnesium deficiency affects roughly half the population and directly impairs sleep by increasing nervous system excitability and reducing GABA activity. GABA is your brain's primary calming neurotransmitter — it's what tells your nervous system to quiet down.

Inflammatory markers. hs-CRP, fasting insulin, fasting glucose, HbA1c. I want the metabolic and inflammatory baseline.

Cortisol rhythm testing. A four-point salivary cortisol test or a DUTCH test — dried urine test for comprehensive hormones — maps cortisol across the entire day so I can see exactly where the rhythm breaks down.

These labs tell me what's actually happening physiologically. And they point directly to what needs fixing, which is always more useful than guessing.

Your Chronotype Matters More Than You Think

One more thing most doctors never address: not everyone is wired for the same sleep schedule.

The cool part is that sleep research has identified distinct chronotypes — essentially your biological predisposition for when you naturally sleep and wake. Some people are early risers. Some are naturally night owls. Some are somewhere in between. Trying to force a night owl into a 10 PM bedtime and 6 AM alarm is fighting biology, and it creates its own stress response.

I don't build sleep protocols around arbitrary "ideal" bedtimes. I work with the patient's natural rhythm and then optimize the physiology around it. Personalized, not prescriptive. Because telling everyone to go to bed at 10 PM is just another version of the one-size-fits-all approach that failed them in the first place.

What I Actually Do About It

Here's my real toolkit — not the generic advice, but what I use in practice:

Fix blood sugar first. Protein and fat at dinner. Minimize refined carbs in the evening. Small bedtime snack if nocturnal hypoglycemia is the pattern. This alone makes a massive difference for a lot of people.

Address cortisol directly. Ashwagandha — an adaptogenic herb — has solid research for reducing cortisol and improving sleep quality. A 2019 randomized controlled trial showed it significantly improved both sleep quality and time to fall asleep compared to placebo. Phosphatidylserine at bedtime can blunt the evening cortisol spike. Magnesium glycinate — 200-400mg at bedtime — calms the nervous system.

Reduce inflammation at the source. This means gut repair, dietary changes, reducing environmental exposures. Omega-3s help. Curcumin helps. But supplementing over a fundamentally inflammatory diet is putting a bandaid on a gunshot wound. You have to address the source.

Morning light exposure. This is genuinely undervalued. Ten to twenty minutes of sunlight within the first hour of waking sets your circadian clock more powerfully than any supplement. It anchors the cortisol peak to the correct time. This is the one sleep hygiene recommendation I push hard, because it actually moves the needle.

Nervous system regulation. If your sympathetic nervous system is stuck in fight-or-flight mode, sleep suffers regardless. I teach patients vagal toning — slow breathing where the exhale is longer than the inhale, cold water face immersion, progressive muscle relaxation. These are tools to shift the nervous system out of overdrive.

And sometimes — going back to the "jumping above the pillars" concept — a patient is too depleted for lifestyle changes to take hold. They need targeted intervention first. Maybe it's correcting a severe ferritin deficiency with IV iron. Maybe it's thyroid optimization. Maybe it's a short course of something pharmacological to break the insomnia cycle so the body can start recovering. The goal is always to get them functional enough that the foundational work can actually stick.

A Word About Sleeping Pills

Let me be direct about prescription sleep medications.

Ambien and similar drugs work by essentially sedating you. They don't produce normal sleep architecture. They reduce the deep, restorative stages of sleep. They're associated with rebound insomnia, dependence, and in long-term use, increased risk of cognitive decline.

I'm not saying never use them. Sometimes patients are so sleep-deprived that they need a pharmacological bridge to break the cycle. But that's exactly what it should be — a bridge, not a destination. The goal is always to identify and fix the root cause so you don't need the medication.

The Bottom Line

Sleep isn't a luxury. Chronic sleep deprivation increases your risk of heart disease, diabetes, obesity, Alzheimer's, depression, and early death. It's not something to manage with a pill. It's something to fix at the root.

If you've tried the hygiene, tried the supplements, tried the prescriptions — and you're still not sleeping — there's a reason. It's almost certainly not a Lunesta deficiency. It's a cortisol problem, a blood sugar problem, an inflammation problem, a nutrient deficiency, or some combination. And those are all things we can test, identify, and fix.

That's what we do at Rooted Health. Come see us.

If you're in Central Texas and ready to get to the root of your sleep issues, [schedule an appointment](https://www.rootedhealthclinic.com) at Rooted Health Clinic.